About Rationally Speaking

Rationally Speaking is a blog maintained by Prof. Massimo Pigliucci, a philosopher at the City University of New York. The blog reflects the Enlightenment figure Marquis de Condorcet's idea of what a public intellectual (yes, we know, that's such a bad word) ought to be: someone who devotes himself to "the tracking down of prejudices in the hiding places where priests, the schools, the government, and all long-established institutions had gathered and protected them." You're welcome. Please notice that the contents of this blog can be reprinted under the standard Creative Commons license.

Wednesday, September 05, 2007

Dembski's friend gets it spectacularly wrong, again

I was waiting for the fellows at the Discovery Institute (the “Intelligent Design” think tank in Seattle) to misuse my recent review in Science of a book on genomics by Michael Lynch of Indiana University. I didn't have to wait long. A contributor to William Dembski's blog, “Uncommon Descent” (isn't that a catchy title?), used my (mild) criticism of Lynch's final chapter in the book to show once again that there is deep disagreement among scientists on evolution. And, as all people of faith know, disagreement is the beginning of the road to Hell, not a healthy sign of intellectual debate.

So, what I actually said of Lynch's book is that it is a must-read for anyone interested in genomics, which is the major topic of the book itself. However, I concentrated my review on the final chapter by Lynch, because it is the most controversial, as he himself clearly says at the beginning of it. That chapter essentially claims that current efforts at significantly expanding the Modern Synthesis (the standard version of evolutionary theory) are misguided because we've got all the theoretical arsenal we need to explain evolution. For Lynch natural selection is but one of several evolutionary “forces,” and not even as central to the evolution of genomes as most people seem to think. Once we add genetic drift, mutation pressure, and all the other staples of population genetics, we've got a pretty complete theory. Lynch dismisses references to newly studied phenomena such as evolvability and modularity, and does not think that evolutionary biologists will uncover any additional organizing principles affecting the history of life.

While Lynch is in very good company, I and several others have in fact called for major expansions of the Modern Synthesis during the past decade or so. Authors such as Mary Jane West-Eberhard, Stephen Gould, Eva Jablonka, Stuart Kauffman, Gerd Muller, Gunter Wagner and many more have pointed out that there are major features of evolution (especially of the evolution of development) that are compatible, yes, but not satisfactorily explained by the Modern Synthesis. Contrary to Lynch's complaints, we have pointed toward several fruitful venues of investigation (including complexity theory, a revised role of constraints in evolution, phenotypic plasticity, and the very same modularity and evolvability referred to above) that might, in our judgment, eventually lead to an Expanded Evolutionary Synthesis.

What has any of this to do with ID? Nothing, of course, since we are talking about a genuine scientific debate which will be settled by the usual means of science: a give-and-take between theory and empirical evidence. But Dembski's blog instead talks about the dangers of reductionism (neither Lynch nor I are reductionists by any stretch of the imagination), and how it does not make any sense “to try to understand a library by studying the alphabet” (has anybody actually suggested that? Besides, surely knowledge of the alphabet is in fact quite important in understanding books, if not libraries...). The post on “Uncommon Descent” shows two pictures of living organisms, a caterpillar and a butterfly, and labels them as two different “proteoms” (i.e., two distinct ensembles of proteins), pointedly asking how can evolution explain the fact that one genome (that of the caterpillar/butterfly) can produce two distinct proteoms.

First off, those are pictures of organisms, not proteoms. Second, there is no mystery: if the author of the post had bothered to read Lynch's book (instead of just my review of it) s/he would know that we have detailed knowledge of how the same genome can produce different proteoms at different developmental stages. And by the way, what would ID's “explanation” be? “God did it?”

“Uncommon Descent” turns into all too common stupidity (or at least intellectual laziness) when the same post pronounces with pseudo-profoundity: “Trying to explain proteomics in terms of genomics is like trying to explain a spacecraft merely as a conglomeration of atoms. It simply fails and is an abysmal category error.” OK, to begin with, the analogy makes no sense: an understanding of genomes (as given by genomics) is a necessary part of the explanation for proteoms (the object of study of proteomics), together with insights provided by other biological disciplines, such as developmental biology. There is no conceptual error at all here, let alone an “abysmal” one. It is just the way science works, and abysmal is only the ignorance of the contributor to that blog. Moreover, the correct philosophical term is “category mistake” (not category error), and it actually means something completely different. The classic example of a category mistake in philosophy is of a fellow being shown the grounds of Oxford University, meeting students, faculty, and administrators, visiting the labs, classrooms and libraries, and at the end of the day saying: “Very interesting, but where is the University?” Clearly he had (mistakenly) thought that the University was something above and beyond the collection of buildings, resources and human beings that make up Oxford. It is, ironically, a mistake that creationists make very readily.

But no bad article on creationism/ID (there is no intellectual difference thereof) would be complete without the most classic of blunders by these pseudo-intellectuals, and I quote: “Trying to comprehend engineering wonders in terms of random accidents makes no sense.” Indeed, it doesn't. But when will you people get it into your thick and ideologically damaged skull that the theory of evolution (even the standard Modern Synthesis version) is not at all based on randomness? What is it in the phrase “natural selection” that makes you think of randomness? “Selection” ain't clear enough for you folks?

20 comments:

I am in Lynch's class right now (he is basically teaching his book) and am looking forward to getting to the part where we will discuss whether pop gen is "enough" to explain the evolution of genomes. Besides some of the books you cite in the review, are there any particularly important studies from the past couple years you recommend reading? Right now, I am tentatively on the Lynch boat, but don't know enough about the subject to be certain. Hopefully no one from the DI will overhear me asking a critical question and post something about the scientific uncertainty of evolution!

it's a small world, isn't it? I just had a private exchange with Michael, I doubt we'll agree on our issues, however.

I suggest reading Dupre's book, The Disorder of Things, for a philosophical critique of population genetics. He may go a bit too far, but he's got excellent points. Lewontin (a population geneticist, as you know) says much of the same in many of his writings (e.g., The Dialectical Biologist).

And of course, if I may, you could take a look at my Making Sense of Evolution, with Jonathan Kaplan.

Heh, M, you're chopping off the hydra's head. IDers are as bad as fundies in being absolutely immune to reason. At least fundies freely admit the religious basis for their ignorance. IDers must be mortified; they adopted the language of science so as to sneak religion into schools, only to find out -- science has no place for god.

"What is it in the phrase “natural selection” that makes you think of randomness? “Selection” ain't clear enough for you folks?"

Yeah, its kind of interesting that the so-called critics of evolutionary theory are so stuck on this idea of "randomness", when it has been so obvious that only a small part of the evolutionary process is random!

But you hear it all the time. "All this could not be random" (presumably the "all this" meaning all of life life). And indeed it isn't. And nobody said it was!

"But when will you people get it into your thick and ideologically damaged skull that the theory of evolution (even the standard Modern Synthesis version) is not at all based on randomness? What is it in the phrase “natural selection” that makes you think of randomness? “Selection” ain't clear enough for you folks?"

Well said. It gets so tiring. The same arguments are made by these freaks over and over and over again no matter how many times they are proven wrong. But then again it really is not about debate with these wackos. It's about promoting their agenda. Their agenda is theocracy and fascism and are using every available means to promote it. It is plain and simple as that.

Have you ever noticed the similarity between the IDers and the Bushies. Prove them wrong time after time and they just keep throwing the same detritus back at you as though it was truth. Unfortunately it all too often works on te American public!

It's no coincidence. IDers are not skeptical of god, despite their pretense to being scientific. They are based on Christianity, as is our current Administration. In religion, doubt is a sin; in the Administration, doubt is a disqualification. Bush et al sadly epitomize my favorite quote, from Frank Herbert:

"Those who see only what they wish are doomed to rot in the stink of their own perceptions."

Dear Prof. Pigliucci,are you in touch with the debate on ID in Italy?In 2004 our Department of Education expunged from the guidelines for teachers the 4 passages dealing with evolution.After a huge protest (by a large group including scientists and Nobel prizes) they declared that everything would be restored.But now I read from the latest Pievani's book that this is not true...

This engineer has no trouble understanding how natural selection turns random mutations into order, complexity and the appearance of "design", but what is a good reference to learn about the other components of this "modern synthesis". I have no post-secondary education in biology, so I am looking for somethng understandable with a basic knowledge of biology.

some of us could care less if a creation historical chronology is thought of as ID or not. Not embarrassed or ashamed about the whole thing one way or another. And why should anyone be? Such a historical chronology is infinitely more pattern and order (other science centered) dependent than evolution ever has been thought to be. Some people may now try to distance themselves from the assumption of randomness in evolution, but most people know that the initial premise of evolution is absolutely one of DISORDER. Origins being, Greek mythology / "Chaos"

But undoubtedly I have mentioned that fact before.

In all honesty, I cannot think of a actual component of nature (except possibly the human mind, which at least has that appearance) that is categorically and or literally random.

Evolutionary biology as we know it started with Darwin who posed a natural mechanism by which order could ascertained out of randomly occurring variation. Darwin called this natural selection. Thus, no evolutionary biologist, from the inception of evolution forward, has suggested that organisms are assembled at random, only that variation accrues through random physical processes. Get a grip!

"some of us could care less if a creation historical chronology is thought of as ID or not."

"but most people know that the initial premise of evolution is absolutely one of DISORDER."

"In all honesty, I cannot think of a actual component of nature (except possibly the human mind, which at least has that appearance) that is categorically and or literally random."

Cal:

1) If Creation is true, it cannot be Intelligent Design; how else can you explain stuff like the appendix or the reversed retina of mammals? From a design standpoint organisms from all phyla are littered with imperfections.

2) You are absolutely wrong about the initial premise of evolution. Darwinian evolution has as its fundamental mechanism non-random selection operating on random mutations. If you roll two dice 100 times and discard all results but boxcars, is your resultant data field random? Certainly not.

3)If you wish to find randomness in nature, look into quantum mechanics.

chris: "..Darwin who posed a natural mechanism by which order could ascertained out of randomly occurring variation"

I PROPOSE that variation is not even anything near random because there is ALWAYS a precise & calculable reason for what is observed. If it happened to be completely unimaginable what might happen next, that may be considered "random". But that is not the case.

wherever one finds explicit instances of repeatability he must not include randomness in "the equation". That's just like interjecting that "fairies did it it" or something.

Actually, we know from direct observation that mutations at the nucleotide level are rather random and certainly not teleological. The fact that organisms respond and that variation changes in a somewhat predictable manner is because of natural selection, which is decidedly non-random and often repeatable.

You can keep saying that evolution is random all you want, but that doesn't mean any actual biologist says that.

"Why would the nucleotide level be thought of as MORE random than other levels of biology? If all things micro are in fact random, then it stands to reason that everything at the macro level HAS TO BE."

Because the copying errors (mutations) occur at the nucleotide level, while selection generally occurs at the level of the organism, as it interacts with the environment. The mutations are not a response to the environment, they simply happen.

Chris: "The mutations are not a response to the environment, they simply happen."

I tend to agree with you, but in the face of it, anti-Darwinian.

Selection is pointless conceptually if the environment only has a marginal effect on the whole biological picture. I can think of a host of physical principles (physics, chemistry before biology) that do in fact take the place of something that SOME people like to call "selection".

Further, it would also be rather a case of "blind faith" to say that errors simply happen. We could also say that the food source ran out, the health of species x was compromised.

That is purely and firstly a physics problem, btw.

As such, we certainly do know the reasons for errors most of the time.

Let's say one had a case of frequent inbreeding in mammals, for instance. Copying errors, of course, become rather predictable at that level. And in the reverse, more distance between breeding and relatedness usually produces fewer copying errors.

etc. etc.

The explanation of 'selection in the gaps' has always been a bit too vague for me.

"Selection is pointless conceptually if the environment only has a marginal effect on the whole biological picture."

Of course the environment has everything to do with selection, but mutations, as far as anyone knows, are random and are independent of the environment. Mutations and selection work in tandem.

"Further, it would also be rather a case of "blind faith" to say that errors simply happen."

Actually this can be observed and measured to a certain extent.

"As such, we certainly do know the reasons for errors most of the time."

The factors you refer to may cause extinction etc., but not copying errors. Inbreeding results in problems because of recombination (2 copies of an allele that is not beneficial, etc.). It is not the cause of mutations.

"I can think of a host of physical principles (physics, chemistry before biology) that do in fact take the place of something that SOME people like to call "selection". "

I think there is probably some truth in this, but one should not make too much of it.

"The explanation of 'selection in the gaps' has always been a bit too vague for me."

I take it you are referring to "Just So stories"? Sure, it is possible to go overboard with interpretations of how adaptations came about. Each "story" is really just an hypothesis, and needs to be tested. But Selection can be observed and measured in some cases, and is a candidate for the explanation of any from or function in biology. Today we can compare entire genomes, and often can specify which genes do what, as well as identify what mutations have been responsible for what changes, so that some of these "just So stories" can be fleshed out to some extent.